In nucleic acid analyses and nucleic acid based therapies, the use of compositions that are similar in structure to naturally occurring nucleotides or their polymers are widely used. For example, in conventional Sanger type nucleic acid sequencing operations, dideoxynucleotides are employed during template directed synthesis, to provide a synthesis termination event associated with a given type of nucleotide. By identifying the relative length of differentially terminated fragments, one can, by comparison to other, shorter and longer synthesized strands, determine the identity and position of the complementary nucleotide in the template sequence. Variations on the Sanger methods include the use of differentially labeled terminators, such that the various fragments in a mixture have a length component to define the relative position of the terminator, as well as a color component to identify at which base synthesis was terminated (See, e.g., U.S. Pat. Nos. 5,821,058 and 5,171,534).
Likewise, nucleotides or polynucleotide probes labeled with complementary members of fluorescent resonant energy transfer dyes, or FRET pairs, are used widely in performing analysis of polymerase chain reactions, in real time (RT-PCR), and in Sanger related sequencing methods. (See U.S. Pat. Nos. 5,688,648, and 6,150,107).
Though a variety of different molecules have been developed that mimic nucleotides and their polymers in a number of different situations, a number of other applications would be opened to such molecules having new and different properties, such as their ability to be recognized and acted upon by enzymes that process such nucleic acids, their stability in reaction mixtures, and the like. The present invention meets these and a variety of other needs.